Croatia in 8 Days

My opinion is that:

If you only visit one island, choose hvar instead of brac. hvar have much more to see, to eat and to experience.

Why not have a walk in krka instead of staying in zadar? Zadar old city needs only half a day to walk around.
I shall spend 2 nights in zadar just because of its good traffic, not the city itself. My goal is krka and plitvice, not the city.

I am assuming you wished to pick up the car in Split. In that case, you could take a catamaran from Dubrovnik to Hvar (http://www.krilo.hr/en/sailing_schedule.html), spend a couple nights, and then go on to Split (see http://www.jadrolinija.hr/ for additional schedules). Depending on where you wished to stay on Brac, you may want to take the bus from Dubrovnik to Split, see Split, and then go to Brac.
The two links I provided will have all of the possible routes you could take. Note a bus goes from Dubrovnik to Korcula also, and then you can go onward to Split from there by boat.
I think I would eliminate Zadar to have more time on the island and to see Split.
What caves are you talking about seeing?

The Barac caves 5 miles from Plitvice.

The best advice we received was to spend the night by Plitvice so you can be at the gate by 7:30 am to avoid the crowds which arrive a bit later. It worked !

I'm one of the people who gives that advice Carla cited. Do not head out from Zadar (which I like a lot), planning to see Plitvice that day. It's unbelievable how crowded the walkways can be when the day-trippers are present. Do whatever you have to do to spend the night at Plitvice before your park visit.

Do you have recommendations for places to stay near Plitvice? Would we need two nights there (night before we visit, as well as the day we visit) or is it feasible to drive to zadar or Zagreb after seeing Plitvice?

I'm a gluten free vegetarian, so trying to stay near bigger cities where food won't be a problem. Thanks!

The reason I warn people to spend the night is that I made the mistake of not doing that and paid a heavy price. Therefore, I cannot provide a personal recommendation for lodging in the area. However, if you go to booking.com you will find a number of options in the area.

I think one night will be fine as long as you get an early start. If you happen to arrive by mid afternoon or so, you might consider getting a 2-day ticket to the park and doing part of your walking that first afternoon/evening. Someone reported here that that worked well. Even if you don't start till the following morning, I believe you'll find that you can see a great deal by mid-afternoon or possibly even earlier. I took the second-longest marked path. I believe it was estimated at 4 hours, but it took me less time despite the mobs. I'd suggest trying the longer walk, but stop at the little shop and buy a trail map so you won't have any trouble finding your way back if you decide not to complete part of the loop.

If you want to push to get away from park fairly early, you might want to pack something for lunch and of course beverages.

There are only 3 authentically approved hotels in the hotel p2 area near Entrance 2. However, there are lots of apartments nearby which you can booked with booking.com or airbnb.
If you are a vegetarian, I suggest you may tried to book an apartment with a kitchen and fridge that you can bring your own vegetables to make your own meals. This must be the healthiest and safe way for your family.

You are trying to squeeze a lot into your time and travelling with my younger children adds another dimension.

A day trip to an island may work best. You don't mention Trogir, which is worth a visit from Split. It's an ambitious schedule.

What places do you highly recommend seeing (how many days at each) and what would you skip?

Unless you are surprisingly unlucky with the weather (I think heavy rain would be unlikely in early September), I view Plitvice as the #1 or #2 sight in Croatia, Dubrovnik being the other place everyone wants to go. I think your children will enjoy Plitvice more than "another old town", but I don't have children of my own and am just guessing about that. I believe having the children along elevates the rank of the caves (again, just guessing) if you can work out the logistics.

Beyond that, I'd be looking at how the pieces fit together. Dubrovnik, Zadar and Zagreb are all nice. The first two have water views that Zagreb lacks. Only you can judge whether they make an island stop non-essential. I'd have no qualms about dropping Zadar for an island, if necessary, though I really enjoyed it; compromises always have to be made. Just be sure 3/4 of your island time isn't spent traveling to and from the island.

Thank you! That's super helpful advice.

If you had to stay in Split or Trogir, what would you recommend?

Also, are there any towns/sights worth seeing while driving from Dubrovnik towards Split?

I haven't been to Trogir, but it's one of the places I've always wanted to go. I think it comes down to how much you value Diocletian's Palace and how you feel about small vs. larger cities. Split's population is about 15 times Trogir's.

We need for someone who has been to Dubrovnik, Trogir and Zadar to come along and tell us how similar they are.

You asked about staying 2 nights around Plitvice.

Just stay in Plitvice the NIGHT before so you can get a head start early. We are big hikers, and even though we stopped to take lots of photos, we still walked every trail and path on the map and left by 2:30 and drove into Split.

Thank you - that's so helpful to know that we only. We'd to stay near plitvice the night before. Any recommendations on where to stay?

Also, between Zadar, Trogir and Split, where would you choose to stay and why?